Top Level Name

  ⌊ Superfamily (core) Radical SAM

    ⌊ Subgroup methyltransferase (Class A)

     ⌊ Family adenosine C2 methyltransferase (RlmN-like)

  ⌊ FunctionalDomain Ribosomal RNA large subunit methyltransferase N (ID 380572)

Superfamily Assignment Evidence Code(s) FSM
Family Assignment Evidence Code CFM PubMed:21527678 PubMed:24806349 PubMed:18025251 PubMed:21415317 PubMed:22891362
This entry was last updated onJune 10, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Escherichia coli str. K-12 substr. MG1655 Taxon ID: 511145 16130442 NP_417012.1 (RefSeq) URP
Taxon ID: 543 445925462 WP_000003317.1 (RefSeq)
Escherichia coli O104:H4 str. 2011C-3493 Taxon ID: 1133852 407480925 YP_006778074.1 (RefSeq) URP
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Uniprot

Protein NameAccessionEC Number Identifier
Dual-specificity RNA methyltransferase RlmN {ECO:0000255|HAMAP-Rule:MF_01849} A7ZPW0 RLMN_ECO24 (Swiss-Prot)
Dual-specificity RNA methyltransferase RlmN {ECO:0000255|HAMAP-Rule:MF_01849} B7UGW3 RLMN_ECO27 (Swiss-Prot)
Dual-specificity RNA methyltransferase RlmN {ECO:0000255|HAMAP-Rule:MF_01849} B7MI02 RLMN_ECO45 (Swiss-Prot)
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Sequence

Length of Enzyme (full-length): 384 | Length of Functional Domain: 365

1       10        20        30        40        50        60

MSEQLVTPENVTTKDGKINLLDLNRQQMREFFKDLGEKPFRADQVMKWMYHYCCDNFDEM
TDINKVLRGKLKEVAEIRAPEVVEEQRSSDGTIKWAIAVGDQRVETVYIPEDDRATLCVS
SQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKVTGQRPITNVVMMGMGE
PLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDE
IRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLK
DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAACGQLAG
DVIDRTKRTLRKRMQGEAIDIKAV
This shows the full-length sequence of the enzyme. The region of the functional domain is highlighted in black letters, while the residual residues are shown in grey. The Superfamily domain, when present, is shown using underlining. In many cases the functional domain is the full-length sequence.
Conserved catalytic residues (as determined by automated alignment to family, subgroup, or superfamily HMMs) are shown with teal highlighting . Conserved catalytic residues which do not matched the Conserved Alignment Residue are shown with maroon highlighting . Information regarding their function can be found in the Conserved Residues section below.
FASTA formatted full-length sequence.
BLAST this sequence against SFLD.
Scan SFLD-HMMs with this sequence.

Conserved Residues
Superfamily CAR This EFD conserves 3/3 Superfamily-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
125 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
129 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
132 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
Subgroup CAR This EFD conserves 5/5 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
118 Cys (C) side chain Nuceophile covalent catalysis -- reactant ISS
125 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
129 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
132 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
355 Cys (C) side chain Nucleophile, Methyl donor covalent catalysis -- reactant ISS
Family CAR This EFD conserves 6/6 Family-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
105 Glu (E) side chain General Acid/Base proton relay -- reactant ICS PubMed:22097883
118 Cys (C) side chain Nucleophile, initiates reductive cleavage of S-S bond covalent catalysis -- reactant IDA PubMed:22097883
125 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ICS PubMed:22097883
129 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ICS PubMed:22097883
132 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ICS PubMed:22097883
355 Cys (C) side chain Nucleophile, forms methylthioether with methyl group from SAM covalent catalysis -- reactant IDA PubMed:22097883

Catalyzed Reaction

23S rRNA (adenine2503-C2)-methyltransferase

2 + + 2 + + + + 2
S-adenosyl-L-methionine zwitterion
59789		 AMP(1-) residue
74411		 di-mu-sulfido-diiron(1+)
33738		 2-methyladenosine 5'-monophosphate(1-) residue
74497		 5'-deoxyadenosine
17319		 L-methionine zwitterion
57844		 S-adenosyl-L-homocysteine zwitterion
57856		 di-mu-sulfido-diiron(2+)
33737

EC: 2.1.1.192 | IntEnz: 2.1.1.192 | Kegg: 2.1.1.192 | BioCyc: 2.1.1.192 | BRENDA: 2.1.1.192

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
3RF9 X-Ray Structure Of Rlmn From Escherichia Coli Ribosomal Rna Large Subunit Methyltransferase N 119 2.2 Iron/Sulfur Cluster • (4R)-2-Methylpentane-2,4-Diol CSA • PDB • PDBSum
3RFA X-Ray Structure Of Rlmn From Escherichia Coli In Complex With S-Adenosylmethionine Ribosomal Rna Large Subunit Methyltransferase N 118 2.05 S-Methylcysteine
(2 more ⇓) 		CSA • PDB • PDBSum
4PL2 X-Ray Crystal Structure Of C118A Rlmn From Escherichia Coli Dual-Specificity Rna Methyltransferase Rlmn 143 2.2 Yes Iron/Sulfur Cluster CSA • PDB • PDBSum
4PL1 X-Ray Crystal Structure Of C118A Rlmn From Escherichia Coli With S-Adenosylmethionine Dual-Specificity Rna Methyltransferase Rlmn 139 2.58 Yes S-Methylcysteine
(2 more ⇓) 		CSA • PDB • PDBSum
Percent identity and alignment length from the BLAST match of the Functional Domain sequence to the PDB sequence.
"Yes" indicates that a GI associated with this Functional Domain was mapped to the PDB ID via UniProtKB.

Curation History
Time Change Annotation Old Value New Value
May 14, 2014, 3:30 a.m. update curation agent holliday setDomainBoundaries.py
update domain end position 384 383
July 15, 2014, 5:16 a.m. update curation agent setDomainBoundaries.py holliday
update name Ribosomal RNA large subunit methyltransferase N Ribosomal RNA large subunit methyltransferase N
Oct. 16, 2014, 5:18 a.m. update curation agent holliday setDomainBoundaries.py
May 11, 2015, 11:33 a.m. update curation agent setDomainBoundaries.py holliday
update curation agent holliday setDomainBoundaries.py
Oct. 15, 2016, 5:09 a.m. update domain end position 383 373
update domain start position 1 9
EC number assigned by UniProtKB accession ID.